make.contigs- Fatal error: Exit code 153 ()

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1

Hi! I have to analyse 16 S RNA sequence from soil and litter. And I’m following the GTN Training - Microbial Analysis - 16S Metagenomics (Tutorial) but the make.contigs step I couldn’t do it. I got this error:

Fatal error: Exit code 153 ()
Tool generated the following standard error:
/data/jwd01/pulsar_staging/60070947/tool_script.sh: line 23: 120 Done echo ‘make.contigs( file=combo_fastq.dat, align=kmer, match=1, mismatch=-1, gapopen=-2, gapextend=-1, rename=True, processors=’${GALAXY_SLOTS:-8}’ )’
121 | sed ‘s/ //g’
122 File size limit exceeded(core dumped) | mothur
123 | tee mothur.out.log

Can you help me to solve this problem?

Thank you in advance

2

Hi @Emilce_Viruel

How big are your files?
Kind regards,
Igor

3

Hi Igor, the files have a size of 15-20 MB each. It´s too much?

4

Nope, the files are small. Have you done QC? What sequencing platform was used?
If you share your history, I can have a look, but it might not be fast. If you have many samples, please copy one sample (two files) into a new history and share it.
You can try one sample on another Galaxy server.
Kind regards,
Igor

5

hi, i have same issue. May i know what size should be fine to run the tools?